The Magpies, with the competition's biggest membership, were ousted by Port Adelaide in an elimination final and Richmond lost to Carlton in the other.
Demetriou said the early exit of two popular Melbourne teams will impact on the AFL's bottom line.
"After the results on the weekend, and they were great results, Fremantle winning (against Geelong) and of course Port Adelaide very gallant and Collingwood out, there's a significant financial hit to the budget of the AFL because of those results," Demetriou told SEN.
"We will be significantly down on budget and when significant I mean seven figures."
Demetriou was critical of the WA Football Commission, who allowed the Australian Rugby Union to book a Wallabies Test match against Argentina this Saturday night at Fremantle's home ground Patersons Stadium.
The Dockers' upset win over Geelong at Simonds Stadium in the qualifying final last Saturday meant that they earned a week off and averted a clash of the codes in Perth.
"That severely compromised the finals," Demetriou said.
"It compromised lots of things about seven and six-day breaks.
"Everyone knows we play finals in September, so putting another code on any day in September is absurd. It doesn't make any sense."
He said that the AFL would like to take control of the fixturing and management of the stadium, but the WAFC has the contract.
"We'd love to (have control), but the problem is that they're contractually obligated as the people who lease that stadium for I think 83 years," he said.
"We've negotiated with the footy commission for a long time on this and it hasn't been a pleasant negotiation.
"I think that decision was a small-minded decision which cost football dearly."
Demetriou added he had spoken to a number of rival clubs about Melbourne's request for a priority draft pick, saying their consistent response had been a resounding "no thanks".
A decision will be made on that by the AFL Commission on September 23.
Demetriou was asked about the response from fans to the AFL's handling and timing of the Essendon supplements saga, which resulted in that club being denied its place in the finals on the eve of the series.
He said the response from surveyed fans had been positive.
"Our early brand tracking shows that in general people are very, very pleased and very grateful about the manner in which we dealt with this matter," he said.
Demetriou agreed that 2013 had been possibly the most difficult in the history of the AFL.
Apart from the Essendon scandal, Adelaide was punished for salary cap and draft tampering and the League investigated Melbourne for alleged tanking.
"This particular issue (Essendon) was probably the most serious affecting the code when you consider we've never seen anything like this and it was a seven or eight-month investigation that was always hovering," he said.
"It hasn't been a great year, you can't sugar coat that.
"Thankfully we restored something on the weekend because people love the footy."
